Primary Citation PubMed: 10525412
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Unleashing the power of meta-threading for evolution/structure-based function inference of proteins.
(2013) Front Genet 4
PubMed: 23802014 | PubMedCentral: PMC3686302 | DOI: 10.3389/fgene.2013.00118
In parentheses are the PDB IDs of weakly homologous (<40% sequence identity) templates identified by e Thread for 2zgm (1c1l, 1d2s, 1g86, 1gzw, 1hdk, 1is3, 1kel, 1kjl, 1kjr, 1lhu, 1lhw, 1ngx, ... qfm, 1qkq, 1slt, 1t2q, 1w6o, 1w6p, 2bkl, 2d03, 2d6m, 2eak, 2eal, 2nmo, 2ny1, 2r0h, 2vno, 2wkk, 2wt0, 2wt1, 2xg3, 2z3z, 2zaa, 2zab, 2zac, 2zhk, 2zhl, 2zhm, 3a71, 3a72, 3ap6, 3ap7, 3gal, 3h3l, 3htl, 3nv3, 3nv4, 3o4h, 4gal); 3mey (1b8a, 1e1t, 1e22, 1e24, 1eqr, 1evk, 1evl, 1fyf, 1kog, 1nyq, 1qf6, 1x54, 1x55, 2cim, 2cja, 2i4o, 2j3m, 2q7e, 2q7g, 2rhq, 2rhs, 2xgt, 2xti, 2zcd, 2zce, 2zin, 3a31, 3a74, 3bju, 3e9h, 3e9i, 3nem, 3qtc); 2fug (1cc1, 1e3d, 1fp4, 1frf, 1frv, 1g20, 1g21, 1h1l, 1h2a, 1h2r, 1l5h, 1l9g, 1m1n, 1m1y, 1m34, 1mio, 1n2c, 1qgu, 1qh1, 1qh8, 1ui0, 1ui1, 1vk2, 1yqw, 1yrq, 2a5h, 2afh, 2afi, 2afk, 2d3y, 2ddg, 2dp6, 2frv, 2min, 2wpn, 2xdq, 3aek, 3aet, 3k1a, 3min, 3myr, 3pdi); 1pue (1if1, 1j59, 1k79, 1lb2, 1o3s, 1run, 1t2k, 1xsd, 1yo5, 2cgp, 3e54, 3jtg); and 2ec2 (1a9n, 1hr6, 1y13, 2a6m, 2a6o, 2ar9, 2vic, 2vih, 2vju, 3a4i, 3a74, 3bju, 3lmb).
Publication Year: 2013
A molecular pathway for the egress of ammonia produced by nitrogenase.
(2013) Sci Rep 3
PubMed: 24241241 | PubMedCentral: PMC3831235 | DOI: 10.1038/srep03237
Calculations of pockets were made for all of the high-resolution crystal structures (PDB 3U7Q, 1M1N, 2MIN, 3MIN, 2AFH, 2AFI, 1MIO, 1QGU, 1QH1, 1QH8, 1H1L) that included the MoFe protein and a high pro... ortion of resolved water molecules (the best structures contain ca 1300 water molecules per FeMo-co in the MoFe protein: structures 3K1A, 1M34 and 2AFK describe considerably less water).
Calculations were made for all of the high-resolution crystal structures (PDB 3U7Q 60 , 1M1N 62 , 2MIN 63 , 3MIN 63 , 2AFH 64 , 2AFI 64 , 1MIO 65 , 1QGU 66 , 1QH1 66 , 1QH8 66 , 1H1L 67 ) that include the MoFe protein and a high proportion of resolved water molecules, and encompassed the species Azotobacter vinelandii ( Av ), Klebsiella pneumoniae ( Kp ) and Clostridium pasteurianum ( Cp ).
For crystal structure 1QGU (residue numbering as in Fig 5 (b) ), the Cα atoms of the helical section of chain A over the reaction face (Val 69 to Cys 61 in 1QGU) have temperature factors well below average, but as the chain continues from residue 58 to lower numbered residues the Cα atom temperature factors increase to well above average, indicative of flexibility as the ammonia efflux extends towards the protein surface.
Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08?Å resolution: comparison with the Azotobacter vinelandii MoFe protein.
(2015) Acta Crystallogr D Biol Crystallogr 71
PubMed: 25664737 | PubMedCentral: PMC4321486 | DOI: 10.1107/S1399004714025243
Additionally, the Klebsiella pneumoniae MoFe protein (Kp1), which is closely related to Av1 with ∼70% sequence identity, has been characterized at 1.6 Å resolution in different... oxidation states (PDB entries 1qh1 in the reduced state, 1qh8 in the oxidized state and 1qgu in the mixed oxidation state; Mayer et al. , 1999 ▶ ).
Publication Year: 2015
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